Contacts of the helix formed by residues 1283 - 1305 (chain A) in PDB entry 6AGF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1283 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241A ALA* 3.8 30.7 - - - +
1243A PHE* 5.4 1.1 - - - -
1278A PHE* 3.6 3.8 + - - -
1279A ILE* 3.3 25.0 + - - +
1281A PHE 3.2 1.0 - - - -
1282A GLY* 1.3 83.2 + - - +
1284A PHE* 1.3 62.6 + - - +
1285A PHE 3.5 0.2 - - - -
1287A LEU* 2.9 34.5 + - - +
1910A 6OU 4.0 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A VAL* 3.9 23.6 - - + -
796A LEU* 4.3 16.6 - - + -
797A PHE* 3.5 49.6 - + + -
800A LEU* 3.7 23.1 - - + -
1279A ILE 3.2 8.2 + - - +
1280A ILE* 3.3 15.0 + - - +
1283A SER* 1.3 77.3 - - - +
1285A PHE* 1.3 75.4 + + - +
1287A LEU* 3.3 5.3 + - - +
1288A ASN* 2.9 28.5 + - - +
1910A 6OU 4.2 38.7 + - + +
1911A 6OU 4.1 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A LEU* 3.8 18.0 - - + +
692A ILE* 3.7 29.3 - - + +
693A ILE* 3.9 15.3 - - + -
696A SER* 3.7 21.1 - - - -
800A LEU* 3.8 24.5 - - + -
1280A ILE* 3.3 30.0 + - + -
1281A PHE* 3.6 43.0 + + - +
1284A PHE* 1.3 87.1 - + - +
1286A THR* 1.3 61.0 + - - +
1288A ASN* 3.2 5.0 + - - +
1289A LEU* 2.9 26.9 + - - +
1910A 6OU 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A LEU* 4.5 7.4 - - - +
1163A VAL* 5.2 0.2 - - - +
1166A VAL* 5.8 2.1 - - - +
1167A CYS* 3.4 35.2 - - + -
1170A PHE* 3.8 18.0 - - - +
1171A TRP* 4.5 2.9 + - - +
1281A PHE 3.5 8.9 + - - -
1282A GLY 3.4 23.3 + - - +
1283A SER 3.8 0.2 + - - -
1284A PHE 3.4 0.4 - - - -
1285A PHE* 1.3 75.9 - - - +
1287A LEU* 1.3 65.5 + - - +
1289A LEU* 3.2 10.1 + - + +
1290A PHE* 2.9 21.7 + - - +
1910A 6OU 3.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A PHE* 4.2 10.1 - - + -
1283A SER 2.9 21.5 + - - +
1284A PHE* 3.5 4.9 - - - +
1286A THR* 1.3 76.6 - - - +
1288A ASN* 1.3 63.5 + - - +
1290A PHE* 3.2 6.7 + - + -
1291A ILE* 3.0 42.5 + - + +
1586A PHE* 4.5 11.2 - - + -
1910A 6OU 3.7 50.9 - - + +
1911A 6OU 4.6 0.4 - - - +
1914A 9Z9 3.5 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ILE* 4.3 16.6 - - + +
797A PHE* 3.5 26.9 - - + +
800A LEU* 2.8 39.1 - - + +
801A LEU* 3.4 31.8 - - - +
804A SER* 5.3 1.6 - - - -
1284A PHE 2.9 14.1 + - - +
1285A PHE* 3.4 12.6 - - - +
1287A LEU* 1.3 78.0 - - - +
1289A LEU* 1.3 61.4 + - - +
1291A ILE* 4.9 0.2 - - - -
1292A GLY* 3.3 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A THR* 4.5 12.8 - - + +
688A MET* 4.5 21.5 - - + -
689A LEU* 4.1 34.5 - - + +
692A ILE* 3.8 16.7 - - + +
1163A VAL* 4.3 18.4 - - + -
1166A VAL* 4.3 18.4 - - + -
1167A CYS* 5.7 1.6 - - - -
1285A PHE 2.9 13.8 + - - +
1286A THR* 3.4 10.1 - - - +
1288A ASN* 1.3 76.7 - - - +
1290A PHE* 1.3 61.8 + - - +
1292A GLY* 3.6 1.4 + - - -
1293A VAL* 3.4 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160A ILE* 4.4 22.7 - - + -
1163A VAL* 3.8 22.9 - - + +
1286A THR 2.9 16.5 + - - +
1287A LEU* 3.6 10.3 - - + +
1289A LEU* 1.3 74.5 - - - +
1291A ILE* 1.3 77.7 + - + +
1293A VAL* 3.5 10.4 + - + +
1294A ILE* 3.4 43.4 + - + +
1586A PHE* 4.2 13.2 - + - -
1587A LEU* 5.7 6.1 - - + -
1590A VAL* 4.1 19.3 - - + -
1910A 6OU 3.5 48.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A PHE* 4.3 10.5 - - + -
801A LEU* 4.1 23.1 - - + -
1287A LEU* 3.0 30.0 + - + +
1288A ASN 4.2 2.7 - - - +
1290A PHE* 1.3 95.4 - - + +
1292A GLY* 1.3 62.4 + - - +
1294A ILE* 3.2 14.4 + - + +
1295A ILE* 3.3 33.1 + - + +
1590A VAL* 4.6 11.9 - - + -
1594A ILE* 5.6 2.7 - - + -
1914A 9Z9 4.1 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A LEU* 3.6 18.7 - - - +
804A SER* 5.2 9.6 - - - -
805A PHE* 5.0 11.2 - - - +
1288A ASN 3.3 11.4 + - - -
1289A LEU 4.2 1.6 - - - -
1290A PHE 3.4 0.2 - - - -
1291A ILE* 1.3 78.8 - - - +
1293A VAL* 1.3 61.4 + - - +
1295A ILE* 4.0 4.4 + - - +
1296A ASP* 3.6 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A THR* 5.7 1.8 - - + -
688A MET* 5.1 9.9 - - - -
1159A SER* 3.9 37.9 - - - +
1160A ILE* 5.6 1.1 - - + -
1163A VAL* 3.7 19.7 - - + -
1289A LEU* 3.4 23.9 + - + +
1290A PHE* 3.5 8.7 + - + +
1291A ILE 3.2 0.8 - - - -
1292A GLY* 1.3 77.5 - - - +
1294A ILE* 1.3 60.5 + - + +
1296A ASP* 3.4 4.2 + - - +
1297A ASN* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156A ALA* 5.7 2.5 - - + -
1159A SER* 5.8 0.2 - - - +
1160A ILE* 5.0 15.5 - - + -
1290A PHE* 3.4 45.3 + - + +
1291A ILE* 3.2 9.5 + - + +
1293A VAL* 1.3 78.5 - - + +
1295A ILE* 1.3 66.1 + - + +
1297A ASN* 3.0 12.1 + - + +
1298A PHE* 2.7 65.9 + - + +
1590A VAL* 4.5 10.5 - - + -
1591A ASN* 5.3 4.5 - - - +
1594A ILE* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A LEU* 6.0 1.1 - - + -
805A PHE* 4.6 19.3 - - + -
1291A ILE* 3.3 43.8 + - + +
1292A GLY* 4.0 3.8 + - - +
1293A VAL 3.4 0.2 - - - -
1294A ILE* 1.3 78.7 - - + +
1296A ASP* 1.3 59.5 + - - +
1298A PHE* 4.3 4.6 - - - +
1299A ASN* 3.0 48.2 + - - +
1594A ILE* 3.9 25.6 - - + -
1598A LEU* 5.1 7.2 - - + -
1914A 9Z9 4.0 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A PHE* 4.6 19.7 - - + +
1292A GLY 3.6 14.5 + - - +
1293A VAL* 3.4 4.3 + - - +
1294A ILE 3.2 0.2 - - - -
1295A ILE* 1.3 78.5 - - + +
1297A ASN* 1.3 63.0 + - - +
1299A ASN* 4.6 8.8 + - - +
1300A GLN* 3.5 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1155A GLY 4.1 5.4 + - - +
1156A ALA* 3.3 32.1 - - - +
1159A SER* 3.2 27.4 + - - +
1293A VAL 2.9 15.0 + - - +
1294A ILE* 3.0 13.7 + - - +
1296A ASP* 1.3 77.2 - - - +
1298A PHE* 1.3 63.5 + - + +
1300A GLN* 3.2 20.1 + - - +
1301A GLN* 2.9 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152A ALA* 4.4 13.9 - - + -
1153A LEU* 5.9 1.1 - - + -
1156A ALA* 4.6 14.8 - - + -
1294A ILE* 2.7 44.2 + - + +
1295A ILE* 4.3 4.3 - - - +
1297A ASN* 1.3 77.1 - - - +
1299A ASN* 1.3 58.5 + - - +
1301A GLN* 3.6 26.3 - - + +
1302A LYS* 3.1 39.8 + - - +
1310A ILE* 5.3 8.4 - - + +
1311A PHE* 4.2 22.9 - + - -
1591A ASN* 3.7 23.8 - - - -
1594A ILE* 3.8 28.0 - - + -
1598A LEU* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1295A ILE* 3.0 26.1 + - - +
1296A ASP* 4.4 10.3 + - - +
1297A ASN 3.2 0.2 - - - -
1298A PHE* 1.3 80.7 - - - +
1300A GLN* 1.3 57.8 + - - +
1302A LYS* 3.5 12.9 + - - +
1303A LYS* 3.0 29.5 + - - +
1598A LEU* 5.2 3.5 - - - +
1914A 9Z9 3.2 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1296A ASP* 3.5 19.0 + - - +
1297A ASN* 3.3 25.1 + - - +
1299A ASN* 1.3 76.3 - - - +
1301A GLN* 1.3 61.9 + - + +
1302A LYS 3.2 1.6 - - - -
1303A LYS* 3.9 5.6 - - - +
1304A LYS* 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A ASN 4.2 2.8 + - - -
1152A ALA* 3.7 34.8 + - - +
1155A GLY* 3.8 19.5 - - - +
1297A ASN* 2.9 29.0 + - - +
1298A PHE* 3.6 29.1 - - + +
1300A GLN* 1.3 77.9 - - + +
1302A LYS* 1.3 58.9 + - - +
1304A LYS* 4.1 9.9 - - - +
1305A LEU* 2.9 51.3 - - + +
1310A ILE* 4.4 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298A PHE* 3.1 34.7 + - - +
1299A ASN* 3.8 12.4 + - - +
1300A GLN 3.2 0.2 - - - -
1301A GLN* 1.3 79.1 - - - +
1303A LYS* 1.3 67.1 + - - +
1305A LEU* 3.7 11.7 - - - +
1307A GLY 4.2 1.4 - - - +
1308A LYS* 3.0 38.0 + - - +
1309A ASP* 4.6 8.3 - - - +
1310A ILE* 4.5 28.0 - - + +
1598A LEU* 5.5 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299A ASN 3.0 18.5 + - - +
1300A GLN* 3.8 6.0 + - - +
1301A GLN 3.6 0.2 - - - -
1302A LYS* 1.3 79.3 - - - +
1304A LYS* 1.3 63.1 + - - +
1308A LYS* 3.8 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1300A GLN* 3.1 19.0 + - - +
1301A GLN* 4.1 7.7 - - - +
1303A LYS* 1.3 78.8 - - - +
1305A LEU* 1.3 101.2 + - + +
1306A GLY* 3.5 1.9 + - - -
1308A LYS* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1301A GLN* 2.9 39.9 + - + +
1302A LYS* 3.7 2.1 + - - +
1303A LYS 3.5 0.4 - - - -
1304A LYS* 1.3 117.1 - - + +
1306A GLY* 1.3 61.1 + - - +
1307A GLY* 3.1 20.7 - - - +
1308A LYS* 2.4 33.8 + - - -
1310A ILE* 5.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il